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Old 02-08-2017, 02:55 PM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,016
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Have you checked to see how much duplication you have in your data? 4000 data tends to have more duplicates if you don't have the right library insert size. Use clumpify.sh from BBMap to get an estimate of total duplicates and optical duplicates. You may not be getting a good assembly if there are too many duplicates.
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